Cocoon’s central government, the Sanctum, holds supreme executive, legislative, and judicial power. It also maintains directive authority over the military.

Despite the fact that Cocoon was built by the fal'Cie, and not by humans, fal'Cie opt to participate only superficially in governmental affairs, leaving Cocoon's administration entirely at the discretion of the human Sanctum and its Primarch, Galenth Dysley.

Sanctum quarantines and exiles anyone from Cocoon whom it believes has been influenced by the outside world. The Sanctum has two main military forces: PSICOM and Guardian Corps, which consist of ordinary soldiers, monsters, automated machines, and military airships.

The Guardian Corps are in charge of domestic issues, while PSICOM is tasked for defending Cocoon from a Gran Pulse invasion. PSICOM is considered superior to the Guardian Corps, but they are deployed less often, leaving them in many regards inexperienced. Notable officers of Sanctum include Yaag Rosch and Jihl Nabaat of PSICOM, and Cid Raines and his subordinate Rygdea of the Cavalry unit of the Guardian Corps.